Why is my Cycles shadow bake all black?
The limitation of baking Shadows is the same currently as with rendering a Shadow Pass in Cycles. The Shadow Pass will only receive its contribution from Blender Lamps. It doesn't work currently with mesh lights, which you are using to emit light into your scene. Try adding a sunlamp just for testing purposes and check if the Shadow Pass then bakes as expected. In my tests here it did. If that works, replacing mesh lights with area lights might be the way to go for you.